Data visualization

Read in lizard data

lizards <- read_csv(here("data_tidy","lizards.csv"))

## Rows: 1628 Columns: 16
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (10): date, scientific_name, common_name, zone, site, plot, spp, sex, rc...
## dbl  (6): pit, toe_num, sv_length, total_length, weight, pc
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

ggplot(data = lizards,
       aes(x = total_length, 
           y = weight)) + 
  geom_point() 

Create a histogram of total lengths for all lizards in the data set

ggplot(data = lizards, 
       aes(x = total_length)) + 
  geom_histogram(bins = 20, 
                 color = "orange", 
                 fill = "purple", 
                 size = 0.2, 
                 linetype = "dotted") 

# IF YOU ARENT CHANGING AN AESTHETIC MAPPED ON A VARIABLE, IT SHOULD NOT BE IN AES 

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(
    shape = 22,
    color = "cyan4",
    fill = "yellow", 
    size = 4, 
    alpha = 0.4 # transparency 
  )

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = common_name, 
                 size = total_length),
             alpha = 0.5) + 
  theme_minimal() 

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = common_name)) + 
  facet_wrap(~common_name) + 
  theme_minimal() 

lizard_total_counts_gbsum <- lizards %>% 
  group_by(common_name) %>%
  summarize(total_count = n())

lizard_total_counts_dplyr <- lizards %>%
  count(common_name)

ggplot(data = lizard_total_counts_gbsum, 
       aes(y = fct_reorder(common_name, -total_count), 
           x = total_count)) + 
  geom_col() 

Create scatterplots, faceted by species common name, for total length versus weight. The color and shape of points should differ based on the species common name. Change the theme. Make each faceted panel have flexible axis limits. (scales should be free)

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = common_name),
             alpha = 0.6,
             size = 1) + 
  facet_wrap(~common_name, 
             scales = "free") +
  labs(x = "Total Length (mm)", 
       y = "Weight (g)",
       title = "Jornada Basin Lizard Sizes",
       subtitle = "all lizards follow the standard length weight relationship with Western Whiptails being largest",
       caption = "Data: Jornada Basin LTER, CCBY")

  theme_minimal()

## List of 93
##  $ line                      :List of 6
##   ..$ colour       : chr "black"
##   ..$ size         : num 0.5
##   ..$ linetype     : num 1
##   ..$ lineend      : chr "butt"
##   ..$ arrow        : logi FALSE
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_line" "element"
##  $ rect                      :List of 5
##   ..$ fill         : chr "white"
##   ..$ colour       : chr "black"
##   ..$ size         : num 0.5
##   ..$ linetype     : num 1
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_rect" "element"
##  $ text                      :List of 11
##   ..$ family       : chr ""
##   ..$ face         : chr "plain"
##   ..$ colour       : chr "black"
##   ..$ size         : num 11
##   ..$ hjust        : num 0.5
##   ..$ vjust        : num 0.5
##   ..$ angle        : num 0
##   ..$ lineheight   : num 0.9
##   ..$ margin       : 'margin' num [1:4] 0points 0points 0points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : logi FALSE
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ title                     : NULL
##  $ aspect.ratio              : NULL
##  $ axis.title                : NULL
##  $ axis.title.x              :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : NULL
##   ..$ vjust        : num 1
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 2.75points 0points 0points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.title.x.top          :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : NULL
##   ..$ vjust        : num 0
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 0points 0points 2.75points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.title.x.bottom       : NULL
##  $ axis.title.y              :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : NULL
##   ..$ vjust        : num 1
##   ..$ angle        : num 90
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 0points 2.75points 0points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.title.y.left         : NULL
##  $ axis.title.y.right        :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : NULL
##   ..$ vjust        : num 0
##   ..$ angle        : num -90
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 0points 0points 0points 2.75points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.text                 :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : chr "grey30"
##   ..$ size         : 'rel' num 0.8
##   ..$ hjust        : NULL
##   ..$ vjust        : NULL
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : NULL
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.text.x               :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : NULL
##   ..$ vjust        : num 1
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 2.2points 0points 0points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.text.x.top           :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : NULL
##   ..$ vjust        : num 0
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 0points 0points 2.2points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.text.x.bottom        : NULL
##  $ axis.text.y               :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : num 1
##   ..$ vjust        : NULL
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 0points 2.2points 0points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.text.y.left          : NULL
##  $ axis.text.y.right         :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : num 0
##   ..$ vjust        : NULL
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 0points 0points 0points 2.2points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ axis.ticks                : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ axis.ticks.x              : NULL
##  $ axis.ticks.x.top          : NULL
##  $ axis.ticks.x.bottom       : NULL
##  $ axis.ticks.y              : NULL
##  $ axis.ticks.y.left         : NULL
##  $ axis.ticks.y.right        : NULL
##  $ axis.ticks.length         : 'simpleUnit' num 2.75points
##   ..- attr(*, "unit")= int 8
##  $ axis.ticks.length.x       : NULL
##  $ axis.ticks.length.x.top   : NULL
##  $ axis.ticks.length.x.bottom: NULL
##  $ axis.ticks.length.y       : NULL
##  $ axis.ticks.length.y.left  : NULL
##  $ axis.ticks.length.y.right : NULL
##  $ axis.line                 : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ axis.line.x               : NULL
##  $ axis.line.x.top           : NULL
##  $ axis.line.x.bottom        : NULL
##  $ axis.line.y               : NULL
##  $ axis.line.y.left          : NULL
##  $ axis.line.y.right         : NULL
##  $ legend.background         : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ legend.margin             : 'margin' num [1:4] 5.5points 5.5points 5.5points 5.5points
##   ..- attr(*, "unit")= int 8
##  $ legend.spacing            : 'simpleUnit' num 11points
##   ..- attr(*, "unit")= int 8
##  $ legend.spacing.x          : NULL
##  $ legend.spacing.y          : NULL
##  $ legend.key                : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ legend.key.size           : 'simpleUnit' num 1.2lines
##   ..- attr(*, "unit")= int 3
##  $ legend.key.height         : NULL
##  $ legend.key.width          : NULL
##  $ legend.text               :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : 'rel' num 0.8
##   ..$ hjust        : NULL
##   ..$ vjust        : NULL
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : NULL
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ legend.text.align         : NULL
##  $ legend.title              :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : num 0
##   ..$ vjust        : NULL
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : NULL
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ legend.title.align        : NULL
##  $ legend.position           : chr "right"
##  $ legend.direction          : NULL
##  $ legend.justification      : chr "center"
##  $ legend.box                : NULL
##  $ legend.box.just           : NULL
##  $ legend.box.margin         : 'margin' num [1:4] 0cm 0cm 0cm 0cm
##   ..- attr(*, "unit")= int 1
##  $ legend.box.background     : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ legend.box.spacing        : 'simpleUnit' num 11points
##   ..- attr(*, "unit")= int 8
##  $ panel.background          : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ panel.border              : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ panel.spacing             : 'simpleUnit' num 5.5points
##   ..- attr(*, "unit")= int 8
##  $ panel.spacing.x           : NULL
##  $ panel.spacing.y           : NULL
##  $ panel.grid                :List of 6
##   ..$ colour       : chr "grey92"
##   ..$ size         : NULL
##   ..$ linetype     : NULL
##   ..$ lineend      : NULL
##   ..$ arrow        : logi FALSE
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_line" "element"
##  $ panel.grid.major          : NULL
##  $ panel.grid.minor          :List of 6
##   ..$ colour       : NULL
##   ..$ size         : 'rel' num 0.5
##   ..$ linetype     : NULL
##   ..$ lineend      : NULL
##   ..$ arrow        : logi FALSE
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_line" "element"
##  $ panel.grid.major.x        : NULL
##  $ panel.grid.major.y        : NULL
##  $ panel.grid.minor.x        : NULL
##  $ panel.grid.minor.y        : NULL
##  $ panel.ontop               : logi FALSE
##  $ plot.background           : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ plot.title                :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : 'rel' num 1.2
##   ..$ hjust        : num 0
##   ..$ vjust        : num 1
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 0points 0points 5.5points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ plot.title.position       : chr "panel"
##  $ plot.subtitle             :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : num 0
##   ..$ vjust        : num 1
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 0points 0points 5.5points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ plot.caption              :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : 'rel' num 0.8
##   ..$ hjust        : num 1
##   ..$ vjust        : num 1
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 5.5points 0points 0points 0points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ plot.caption.position     : chr "panel"
##  $ plot.tag                  :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : 'rel' num 1.2
##   ..$ hjust        : num 0.5
##   ..$ vjust        : num 0.5
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : NULL
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ plot.tag.position         : chr "topleft"
##  $ plot.margin               : 'margin' num [1:4] 5.5points 5.5points 5.5points 5.5points
##   ..- attr(*, "unit")= int 8
##  $ strip.background          : list()
##   ..- attr(*, "class")= chr [1:2] "element_blank" "element"
##  $ strip.background.x        : NULL
##  $ strip.background.y        : NULL
##  $ strip.placement           : chr "inside"
##  $ strip.text                :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : chr "grey10"
##   ..$ size         : 'rel' num 0.8
##   ..$ hjust        : NULL
##   ..$ vjust        : NULL
##   ..$ angle        : NULL
##   ..$ lineheight   : NULL
##   ..$ margin       : 'margin' num [1:4] 4.4points 4.4points 4.4points 4.4points
##   .. ..- attr(*, "unit")= int 8
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ strip.text.x              : NULL
##  $ strip.text.y              :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : NULL
##   ..$ vjust        : NULL
##   ..$ angle        : num -90
##   ..$ lineheight   : NULL
##   ..$ margin       : NULL
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  $ strip.switch.pad.grid     : 'simpleUnit' num 2.75points
##   ..- attr(*, "unit")= int 8
##  $ strip.switch.pad.wrap     : 'simpleUnit' num 2.75points
##   ..- attr(*, "unit")= int 8
##  $ strip.text.y.left         :List of 11
##   ..$ family       : NULL
##   ..$ face         : NULL
##   ..$ colour       : NULL
##   ..$ size         : NULL
##   ..$ hjust        : NULL
##   ..$ vjust        : NULL
##   ..$ angle        : num 90
##   ..$ lineheight   : NULL
##   ..$ margin       : NULL
##   ..$ debug        : NULL
##   ..$ inherit.blank: logi TRUE
##   ..- attr(*, "class")= chr [1:2] "element_text" "element"
##  - attr(*, "class")= chr [1:2] "theme" "gg"
##  - attr(*, "complete")= logi TRUE
##  - attr(*, "validate")= logi TRUE

Fun with scales

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = weight)) + 
  scale_color_gradient(low = "orange", high = "purple") 

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = weight)) + 
  scale_color_gradientn(colors = c("magenta","cyan4","darkorchid3","dodgerblue","green","yellow")) 

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = weight)) + 
  scale_color_steps(low = "red", high = "black") 

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = total_length)) + 
  scale_color_steps2(low = "purple", 
                     mid = "white",
                     high = "orange", 
                     midpoint = 150,
                     breaks = c(50, 75, 150, 180, 220, 280))

ggplot(data = lizards, 
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = total_length)) + 
  scale_color_stepsn(colors = c("orange", "red", "purple"), 
                     breaks = seq(from = 0, to = 300, by = 60))

Make a horizontal box plot with common name on the y-axis, total length on the x axis, fill changing based on the common name

lizards_median <- lizards %>% 
  mutate(common_name = fct_reorder(common_name, total_length, .fun = median)) # create a new column which overwrites an existing column, recasting common name as a factor. then reorder common names based on the median of total length for each of the different levels of the factor ---- common name in this case. 

ggplot(data = lizards,
       aes(x = total_length,
           y = common_name)) + 
  geom_boxplot(aes(fill = common_name))

ggplot(data = lizards_median,
       aes(y = common_name, 
           x = total_length)) + 
  geom_boxplot(aes(fill = common_name), show.legend = FALSE) + 
  scale_fill_paletteer_d(palette = "yarrr::southpark") + 
  theme_minimal() 

palette_options <- palettes_d_names

ugly plot

ggplot(data = lizards,
       aes(x = total_length,
           y = weight)) + 
  geom_point(aes(color = weight)) + 
  theme(panel.grid.major.x = element_line(color = "red"),
        panel.grid.minor.y = element_blank(), 
        axis.title = element_text(color = "purple"), 
        axis.text.y = element_text(color = "green"),
        text = element_text(size = 18), 
        panel.background = element_rect(color = "purple", 
                                        fill = "green")) + 
  annotate("text", x = 300, y = 50, label = "Wooooo\ntest", color = "blue") + 
  geom_vline(xintercept = 250, linetype = "dashed", color = "orange", size = 4)

repulsive labels with ggrepel

wws_lizards <- lizards %>%
  filter(common_name == "western whiptail", 
         site == "sand") 

ggplot(data = wws_lizards,
       aes(x = total_length,
           y = weight)) + 
  geom_point() + 
  geom_text_repel(aes(label = toe_num))

gapminder %>% 
  filter(year == 2002, continent == "Europe") %>%
  ggplot(aes(x = gdpPercap, y = lifeExp)) + 
  geom_point() + 
  geom_text_repel(aes(label = country), size = 3)

ggplot(data = lizards,
       aes(x = total_length,
           y = weight)) + 
  geom_point() + 
  gghighlight(weight > 30, label_key = toe_num)

Make a map!

jornada_veg <- sf::read_sf(here("data_raw","spatial_vegetation","doc.kml"))

ggplot(data = jornada_veg) + 
  geom_sf(aes(fill = Name)) +
  theme_minimal() + 
  scale_fill_paletteer_d(palette = "ggthemes::manyeys")

Day 10 stuff!

Make a heat map

lizard_counts <- lizards %>% 
  mutate(date = lubridate::mdy(date)) %>%
  count(year = lubridate::year(date), common_name) %>% # for each year of the dataset, i have the count for each lizard species 
  drop_na() 

ggplot(data = lizard_counts, aes(x = year, y = common_name)) + 
  geom_tile(aes(fill = n), show.legend = FALSE) + 
  geom_text(aes(label = n), color = "white", size = 3) + 
  scale_fill_gradientn(colors = c("navy","red","orange")) + 
  theme_minimal() 

Beeswarm plot

whiptails <- lizards %>%
  filter(common_name == "western whiptail") %>%
  drop_na(total_length, weight)

whiptail_bee <- ggplot(data = whiptails, 
       aes(x = sex, 
           y = weight)) + 
  ggbeeswarm::geom_beeswarm(size = 0.5) + 
  geom_boxplot(fill = NA)

whiptail_plot <- ggplot(data = whiptails, 
       aes(x = total_length, 
           y = weight)) + 
  geom_point(aes(color = sex)) + 
  theme(legend.position = "bottom")

ggMarginal(whiptail_plot, type = "boxplot", groupColour = TRUE)

Patchwork – addition creates columns, division creates rows

((whiptail_bee + whiptail_plot) / whiptail_bee) + whiptail_plot